Sodium in PDB 3jr7: The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149

The structure of The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149, PDB code: 3jr7 was solved by R.Zhang, C.Hatzos, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.92 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.899, 96.899, 159.921, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 20.8

The binding sites of Sodium atom in the The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149 (pdb code 3jr7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149, PDB code: 3jr7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:51.4 occ:1.00 NE A:ARG224 3.4 36.4 1.0 NH2 A:ARG224 3.6 34.2 1.0 CD1 A:ILE205 3.8 35.8 1.0 CZ A:ARG224 4.0 35.2 1.0 CG1 A:ILE205 4.3 36.1 1.0 CG A:ARG224 4.3 32.3 1.0 CD A:ARG224 4.5 35.0 1.0 CE A:LYS222 4.6 40.4 1.0 NZ A:LYS222 4.9 44.3 1.0 CB A:ALA202 5.0 45.4 1.0

Sodium binding site 2 out of 4 in the The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:45.0 occ:1.00 N A:ARG224 3.8 27.8 1.0 NZ A:LYS232 3.8 29.7 1.0 CA A:ALA223 3.9 27.4 1.0 CB A:ALA223 4.1 26.1 1.0 CE A:LYS232 4.1 30.5 1.0 CD A:LYS228 4.3 36.2 1.0 C A:ALA223 4.4 27.5 1.0 NZ A:LYS228 4.7 44.2 1.0 O A:LYS222 4.7 27.6 1.0 CB A:ARG224 4.8 29.3 1.0 CG A:ARG224 4.8 32.3 1.0 CA A:ARG224 4.8 28.3 1.0 CB A:LYS228 5.0 25.5 1.0

Sodium binding site 3 out of 4 in the The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:65.2 occ:1.00 O A:HOH426 3.1 55.0 1.0 NE A:ARG87 3.2 47.0 1.0 NH2 A:ARG87 3.6 42.0 1.0 CZ A:ARG87 3.8 46.1 1.0 OG A:SER84 4.0 23.9 1.0 CD A:ARG87 4.1 42.0 1.0 CB A:SER84 4.4 26.0 1.0

Sodium binding site 4 out of 4 in the The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:57.1 occ:1.00 O B:HOH448 3.2 38.4 1.0 O B:HOH580 3.4 63.9 1.0 N B:CYS77 3.4 30.9 1.0 CB B:CYS77 3.8 31.8 1.0 O B:HOH579 4.0 68.5 1.0 CA B:SER76 4.0 33.5 1.0 C B:SER76 4.2 31.7 1.0 CA B:CYS77 4.2 31.0 1.0 CB B:SER76 4.5 33.5 1.0 O B:THR75 4.7 35.5 1.0 O B:CYS77 4.9 28.1 1.0 OG B:SER76 4.9 38.6 1.0 CD B:LYS188 4.9 40.5 1.0

R.Zhang, C.Hatzos, S.Clancy, A.Joachimiak. The Crystal Structure of the Protein of Degv Family COG1307 with Unknown Function From Ruminococcus Gnavus Atcc 29149 To Be Published.